Starting phenix.real_space_refine on Fri Sep 11 19:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.map" model { file = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n52_0346/09_2026/6n52_0346.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 7096 2.51 5 N 1878 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 14, 'GLU:plan': 20, 'ARG:plan': 10, 'ASN:plan1': 8, 'PHE:plan': 6, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 325 Chain: "B" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5526 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 740} Chain breaks: 2 Unresolved non-hydrogen bonds: 598 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 494 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 14, 'GLU:plan': 20, 'ARG:plan': 10, 'ASN:plan1': 8, 'PHE:plan': 6, 'GLN:plan1': 8, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 325 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.62, per 1000 atoms: 0.24 Number of scatterers: 11108 At special positions: 0 Unit cell: (117.66, 79.5, 183.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2026 8.00 N 1878 7.00 C 7096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.04 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG A 902 " - " ASN A 445 " " NAG B 901 " - " ASN B 210 " " NAG B 902 " - " ASN B 445 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 564.3 milliseconds 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2892 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 47.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.945A pdb=" N VAL A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 122 Processing helix chain 'A' and resid 151 through 163 removed outlier: 4.120A pdb=" N GLN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.706A pdb=" N VAL A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 236 removed outlier: 3.645A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 227 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 236 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 294 Processing helix chain 'A' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA A 308 " --> pdb=" O ASP A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.540A pdb=" N ASP A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 removed outlier: 3.708A pdb=" N VAL A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 401 " --> pdb=" O MET A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.819A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA A 582 " --> pdb=" O PRO A 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 636 removed outlier: 4.044A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A 651 " --> pdb=" O GLN A 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 652 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Proline residue: A 655 - end of helix removed outlier: 3.663A pdb=" N SER A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 661 " --> pdb=" O MET A 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 715 removed outlier: 4.243A pdb=" N ALA A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 761 Proline residue: A 743 - end of helix removed outlier: 3.594A pdb=" N TYR A 746 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 794 removed outlier: 6.264A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 786 " --> pdb=" O CYS A 782 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL A 789 " --> pdb=" O TRP A 785 " (cutoff:3.500A) Proline residue: A 790 - end of helix Processing helix chain 'A' and resid 799 through 816 removed outlier: 3.757A pdb=" N VAL A 806 " --> pdb=" O MET A 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER A 807 " --> pdb=" O CYS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 832 removed outlier: 3.698A pdb=" N ARG A 831 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASN A 832 " --> pdb=" O PRO A 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 828 through 832' Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.944A pdb=" N VAL B 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 122 Processing helix chain 'B' and resid 151 through 163 removed outlier: 4.119A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 160 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 195 through 210 removed outlier: 3.707A pdb=" N VAL B 206 " --> pdb=" O MET B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 3.644A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 227 " --> pdb=" O TYR B 223 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 294 Processing helix chain 'B' and resid 305 through 308 removed outlier: 3.609A pdb=" N ALA B 308 " --> pdb=" O ASP B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 334 through 343 removed outlier: 3.541A pdb=" N ASP B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 363 removed outlier: 3.729A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 removed outlier: 3.707A pdb=" N VAL B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 434 through 443 removed outlier: 3.818A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 removed outlier: 3.988A pdb=" N ALA B 582 " --> pdb=" O PRO B 578 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.689A pdb=" N SER B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 636 removed outlier: 4.045A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 668 removed outlier: 4.082A pdb=" N GLY B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 651 " --> pdb=" O GLN B 647 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 652 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Proline residue: B 655 - end of helix removed outlier: 3.664A pdb=" N SER B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 661 " --> pdb=" O MET B 657 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 662 " --> pdb=" O SER B 658 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 715 removed outlier: 4.244A pdb=" N ALA B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 698 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 714 " --> pdb=" O ALA B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 761 Proline residue: B 743 - end of helix removed outlier: 3.595A pdb=" N TYR B 746 " --> pdb=" O THR B 742 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 765 through 794 removed outlier: 6.265A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 773 " --> pdb=" O ASN B 769 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 783 " --> pdb=" O TYR B 779 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 786 " --> pdb=" O CYS B 782 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 789 " --> pdb=" O TRP B 785 " (cutoff:3.500A) Proline residue: B 790 - end of helix Processing helix chain 'B' and resid 799 through 816 removed outlier: 3.758A pdb=" N VAL B 806 " --> pdb=" O MET B 802 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER B 807 " --> pdb=" O CYS B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 832 removed outlier: 3.697A pdb=" N ARG B 831 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 832 " --> pdb=" O PRO B 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 828 through 832' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU A 94 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 41 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE A 36 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY A 145 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR A 246 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 216 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE A 248 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS A 218 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL A 273 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 277 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR A 219 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP A 487 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASN A 470 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN A 483 " --> pdb=" O ASN A 470 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LYS A 472 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR A 481 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 3.686A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 521 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AB2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.801A pdb=" N GLU B 94 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 41 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 36 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY B 145 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 241 through 242 removed outlier: 9.831A pdb=" N TYR B 246 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA B 216 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ILE B 248 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 218 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 242 removed outlier: 6.008A pdb=" N VAL B 273 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 277 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR B 219 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 325 through 329 removed outlier: 3.582A pdb=" N TRP B 487 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 470 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ASN B 483 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS B 472 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B 481 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 447 removed outlier: 3.685A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 520 through 521 Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AC1, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AC2, first strand: chain 'B' and resid 719 through 720 526 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3598 1.34 - 1.46: 2698 1.46 - 1.58: 4910 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 11358 Sorted by residual: bond pdb=" C SER A 654 " pdb=" N PRO A 655 " ideal model delta sigma weight residual 1.337 1.365 -0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C SER B 654 " pdb=" N PRO B 655 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.24e-02 6.50e+03 4.82e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C1 NAG A 902 " pdb=" O5 NAG A 902 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 11353 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 15063 1.75 - 3.50: 397 3.50 - 5.26: 36 5.26 - 7.01: 16 7.01 - 8.76: 10 Bond angle restraints: 15522 Sorted by residual: angle pdb=" C VAL A 499 " pdb=" N TRP A 500 " pdb=" CA TRP A 500 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C VAL B 499 " pdb=" N TRP B 500 " pdb=" CA TRP B 500 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" N VAL B 191 " pdb=" CA VAL B 191 " pdb=" C VAL B 191 " ideal model delta sigma weight residual 112.29 108.05 4.24 9.40e-01 1.13e+00 2.04e+01 angle pdb=" N VAL A 191 " pdb=" CA VAL A 191 " pdb=" C VAL A 191 " ideal model delta sigma weight residual 112.29 108.10 4.19 9.40e-01 1.13e+00 1.99e+01 angle pdb=" N ILE B 824 " pdb=" CA ILE B 824 " pdb=" C ILE B 824 " ideal model delta sigma weight residual 111.91 109.21 2.70 8.90e-01 1.26e+00 9.17e+00 ... (remaining 15517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 6458 15.26 - 30.53: 170 30.53 - 45.79: 64 45.79 - 61.06: 0 61.06 - 76.32: 4 Dihedral angle restraints: 6696 sinusoidal: 2200 harmonic: 4496 Sorted by residual: dihedral pdb=" CB CYS A 241 " pdb=" SG CYS A 241 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS B 241 " pdb=" SG CYS B 241 " pdb=" SG CYS B 530 " pdb=" CB CYS B 530 " ideal model delta sinusoidal sigma weight residual -86.00 -150.69 64.69 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CA PHE A 804 " pdb=" C PHE A 804 " pdb=" N SER A 805 " pdb=" CA SER A 805 " ideal model delta harmonic sigma weight residual -180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 6693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1078 0.035 - 0.070: 494 0.070 - 0.105: 184 0.105 - 0.140: 55 0.140 - 0.175: 9 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB VAL A 610 " pdb=" CA VAL A 610 " pdb=" CG1 VAL A 610 " pdb=" CG2 VAL A 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 610 " pdb=" CA VAL B 610 " pdb=" CG1 VAL B 610 " pdb=" CG2 VAL B 610 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA SER B 654 " pdb=" N SER B 654 " pdb=" C SER B 654 " pdb=" CB SER B 654 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1817 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 577 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO B 578 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 578 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 578 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 577 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 578 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 779 " -0.009 2.00e-02 2.50e+03 1.32e-02 3.48e+00 pdb=" CG TYR B 779 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 779 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 779 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 779 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 779 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 779 " 0.002 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3682 2.84 - 3.36: 10215 3.36 - 3.87: 18278 3.87 - 4.39: 19558 4.39 - 4.90: 33371 Nonbonded interactions: 85104 Sorted by model distance: nonbonded pdb=" OH TYR B 223 " pdb=" OD1 ASP B 305 " model vdw 2.328 3.040 nonbonded pdb=" OH TYR A 223 " pdb=" OD1 ASP A 305 " model vdw 2.329 3.040 nonbonded pdb=" NE2 GLN A 163 " pdb=" O LEU A 184 " model vdw 2.334 3.120 nonbonded pdb=" NE2 GLN B 163 " pdb=" O LEU B 184 " model vdw 2.335 3.120 nonbonded pdb=" OG SER B 176 " pdb=" OD1 ASP B 178 " model vdw 2.340 3.040 ... (remaining 85099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11382 Z= 0.183 Angle : 0.715 10.608 15574 Z= 0.401 Chirality : 0.046 0.175 1820 Planarity : 0.006 0.051 1992 Dihedral : 8.418 76.320 3744 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.16), residues: 1536 helix: -2.63 (0.14), residues: 688 sheet: -2.65 (0.36), residues: 162 loop : -2.82 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 291 TYR 0.032 0.002 TYR B 779 PHE 0.027 0.002 PHE A 165 TRP 0.022 0.003 TRP A 307 HIS 0.007 0.001 HIS B 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.18 (11358) covalent geometry : angle 0.69852 / 0.40 (15522) SS BOND : bond 0.00252 / 0.15 ( 20) SS BOND : angle 0.85633 / 0.57 ( 40) hydrogen bonds : bond 0.15758 / 11.17 ( 524) hydrogen bonds : angle 6.39049 / 4.33 ( 1512) link_NAG-ASN : bond 0.00361 / 0.18 ( 4) link_NAG-ASN : angle 5.49700 / 2.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 TYR cc_start: 0.8213 (p90) cc_final: 0.7929 (p90) REVERT: A 778 MET cc_start: 0.8348 (mmm) cc_final: 0.7787 (tpp) REVERT: A 802 MET cc_start: 0.9143 (ttm) cc_final: 0.8694 (ppp) REVERT: B 442 MET cc_start: 0.8204 (tpp) cc_final: 0.7985 (tpt) REVERT: B 778 MET cc_start: 0.8299 (mmm) cc_final: 0.7743 (tpp) REVERT: B 802 MET cc_start: 0.9159 (ttm) cc_final: 0.8708 (ppp) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0791 time to fit residues: 14.5913 Evaluate side-chains 69 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS A 218 HIS A 704 GLN B 101 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS B 704 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.061630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042872 restraints weight = 77395.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.043859 restraints weight = 45060.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.044584 restraints weight = 30191.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.045068 restraints weight = 23344.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045277 restraints weight = 19671.961| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11382 Z= 0.191 Angle : 0.612 11.149 15574 Z= 0.315 Chirality : 0.042 0.146 1820 Planarity : 0.005 0.053 1992 Dihedral : 4.225 15.367 1650 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.78 % Allowed : 6.15 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.20), residues: 1536 helix: -0.69 (0.18), residues: 688 sheet: -2.21 (0.36), residues: 186 loop : -1.95 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.015 0.001 TYR B 209 PHE 0.019 0.002 PHE B 165 TRP 0.011 0.002 TRP A 211 HIS 0.004 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (11358) covalent geometry : angle 0.60414 / 0.31 (15522) SS BOND : bond 0.00210 / 0.13 ( 20) SS BOND : angle 1.05618 / 0.78 ( 40) hydrogen bonds : bond 0.03063 / 2.18 ( 524) hydrogen bonds : angle 4.70150 / 3.19 ( 1512) link_NAG-ASN : bond 0.00077 / 0.04 ( 4) link_NAG-ASN : angle 3.22490 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.546 Fit side-chains REVERT: A 414 MET cc_start: 0.8882 (ttm) cc_final: 0.8492 (mtt) REVERT: A 778 MET cc_start: 0.8265 (mmm) cc_final: 0.7516 (tmm) REVERT: A 802 MET cc_start: 0.9235 (ttm) cc_final: 0.8871 (ppp) REVERT: B 414 MET cc_start: 0.8936 (ttm) cc_final: 0.8565 (mtt) REVERT: B 778 MET cc_start: 0.8226 (mmm) cc_final: 0.7738 (tpp) REVERT: B 802 MET cc_start: 0.9241 (ttm) cc_final: 0.8874 (ppp) outliers start: 8 outliers final: 2 residues processed: 82 average time/residue: 0.0802 time to fit residues: 10.4397 Evaluate side-chains 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 48 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 3 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 overall best weight: 2.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.061592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.042736 restraints weight = 76154.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.043752 restraints weight = 45119.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.044450 restraints weight = 30292.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.044941 restraints weight = 23294.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.045167 restraints weight = 19574.844| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11382 Z= 0.145 Angle : 0.561 8.159 15574 Z= 0.284 Chirality : 0.042 0.202 1820 Planarity : 0.004 0.049 1992 Dihedral : 4.051 14.701 1650 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.68 % Allowed : 6.15 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1536 helix: 0.15 (0.19), residues: 692 sheet: -2.02 (0.37), residues: 188 loop : -1.63 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 668 TYR 0.009 0.001 TYR B 209 PHE 0.014 0.001 PHE B 165 TRP 0.008 0.001 TRP B 557 HIS 0.003 0.001 HIS A 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (11358) covalent geometry : angle 0.55395 / 0.28 (15522) SS BOND : bond 0.00129 / 0.08 ( 20) SS BOND : angle 0.79627 / 0.59 ( 40) hydrogen bonds : bond 0.02861 / 2.06 ( 524) hydrogen bonds : angle 4.46954 / 2.99 ( 1512) link_NAG-ASN : bond 0.00181 / 0.09 ( 4) link_NAG-ASN : angle 3.02720 / 1.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.440 Fit side-chains REVERT: A 72 MET cc_start: 0.9341 (ttp) cc_final: 0.8822 (ppp) REVERT: A 189 MET cc_start: 0.8459 (mmt) cc_final: 0.7891 (mmm) REVERT: A 469 MET cc_start: 0.8744 (mmm) cc_final: 0.8158 (mmm) REVERT: A 482 ILE cc_start: 0.9614 (OUTLIER) cc_final: 0.9382 (pt) REVERT: A 778 MET cc_start: 0.8291 (mmm) cc_final: 0.7553 (tmm) REVERT: A 802 MET cc_start: 0.9243 (ttm) cc_final: 0.8893 (ppp) REVERT: B 72 MET cc_start: 0.9333 (ttp) cc_final: 0.8819 (ppp) REVERT: B 189 MET cc_start: 0.8377 (mmt) cc_final: 0.8094 (mmm) REVERT: B 438 LEU cc_start: 0.9588 (tp) cc_final: 0.9359 (mm) REVERT: B 469 MET cc_start: 0.8712 (mmm) cc_final: 0.8141 (mmm) REVERT: B 482 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9386 (pt) REVERT: B 778 MET cc_start: 0.8226 (mmm) cc_final: 0.7503 (tmm) REVERT: B 802 MET cc_start: 0.9260 (ttm) cc_final: 0.8919 (ppp) outliers start: 7 outliers final: 2 residues processed: 75 average time/residue: 0.0803 time to fit residues: 9.9376 Evaluate side-chains 66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 482 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 8 optimal weight: 2.9990 chunk 138 optimal weight: 0.0870 chunk 1 optimal weight: 9.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN B 163 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.062209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.043630 restraints weight = 74994.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.044639 restraints weight = 44973.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.045348 restraints weight = 30337.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.045891 restraints weight = 23162.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.046249 restraints weight = 19173.339| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11382 Z= 0.097 Angle : 0.512 7.251 15574 Z= 0.257 Chirality : 0.041 0.290 1820 Planarity : 0.003 0.045 1992 Dihedral : 3.850 13.445 1650 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.88 % Allowed : 6.64 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.22), residues: 1536 helix: 0.63 (0.19), residues: 694 sheet: -2.10 (0.34), residues: 208 loop : -1.58 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.007 0.001 TYR A 340 PHE 0.012 0.001 PHE A 165 TRP 0.008 0.001 TRP A 557 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (11358) covalent geometry : angle 0.50682 / 0.26 (15522) SS BOND : bond 0.00087 / 0.06 ( 20) SS BOND : angle 0.65479 / 0.47 ( 40) hydrogen bonds : bond 0.02515 / 1.79 ( 524) hydrogen bonds : angle 4.34004 / 2.89 ( 1512) link_NAG-ASN : bond 0.00218 / 0.11 ( 4) link_NAG-ASN : angle 2.63704 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8940 (ppp) REVERT: A 202 MET cc_start: 0.9167 (mmt) cc_final: 0.8871 (mmt) REVERT: A 234 MET cc_start: 0.8753 (mtp) cc_final: 0.8503 (mtp) REVERT: A 778 MET cc_start: 0.8295 (mmm) cc_final: 0.7602 (tmm) REVERT: A 802 MET cc_start: 0.9275 (ttm) cc_final: 0.8908 (ppp) REVERT: B 72 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.8919 (ppp) REVERT: B 202 MET cc_start: 0.9158 (mmt) cc_final: 0.8856 (mmt) REVERT: B 234 MET cc_start: 0.8753 (mtp) cc_final: 0.8506 (mtp) REVERT: B 778 MET cc_start: 0.8235 (mmm) cc_final: 0.7550 (tmm) REVERT: B 802 MET cc_start: 0.9292 (ttm) cc_final: 0.8931 (ppp) outliers start: 9 outliers final: 2 residues processed: 70 average time/residue: 0.0887 time to fit residues: 9.6946 Evaluate side-chains 68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 82 optimal weight: 0.0040 chunk 122 optimal weight: 5.9990 overall best weight: 3.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.060375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.041655 restraints weight = 75332.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.042651 restraints weight = 44852.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.043348 restraints weight = 30395.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.043814 restraints weight = 23399.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.044104 restraints weight = 19597.394| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11382 Z= 0.174 Angle : 0.576 7.049 15574 Z= 0.292 Chirality : 0.042 0.147 1820 Planarity : 0.004 0.044 1992 Dihedral : 3.982 14.137 1650 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.59 % Allowed : 7.32 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1536 helix: 0.74 (0.19), residues: 698 sheet: -1.94 (0.36), residues: 188 loop : -1.38 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 362 TYR 0.008 0.001 TYR A 340 PHE 0.014 0.001 PHE B 165 TRP 0.008 0.001 TRP B 557 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (11358) covalent geometry : angle 0.57050 / 0.29 (15522) SS BOND : bond 0.00148 / 0.09 ( 20) SS BOND : angle 0.57666 / 0.40 ( 40) hydrogen bonds : bond 0.02770 / 2.02 ( 524) hydrogen bonds : angle 4.54705 / 3.05 ( 1512) link_NAG-ASN : bond 0.00185 / 0.10 ( 4) link_NAG-ASN : angle 2.91687 / 1.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.460 Fit side-chains REVERT: A 72 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8938 (ppp) REVERT: A 202 MET cc_start: 0.9124 (mmt) cc_final: 0.8812 (mmt) REVERT: A 778 MET cc_start: 0.8271 (mmm) cc_final: 0.7596 (tmm) REVERT: A 802 MET cc_start: 0.9318 (ttm) cc_final: 0.8945 (tmm) REVERT: B 72 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8928 (ppp) REVERT: B 202 MET cc_start: 0.9119 (mmt) cc_final: 0.8783 (mmt) REVERT: B 778 MET cc_start: 0.8236 (mmm) cc_final: 0.7555 (tmm) REVERT: B 802 MET cc_start: 0.9310 (ttm) cc_final: 0.8937 (tmm) outliers start: 6 outliers final: 2 residues processed: 66 average time/residue: 0.0811 time to fit residues: 8.8804 Evaluate side-chains 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 78 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.060506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.041833 restraints weight = 75151.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.042718 restraints weight = 43042.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.043459 restraints weight = 30492.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.043996 restraints weight = 23708.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.044141 restraints weight = 19647.911| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11382 Z= 0.158 Angle : 0.570 10.615 15574 Z= 0.285 Chirality : 0.041 0.135 1820 Planarity : 0.004 0.044 1992 Dihedral : 3.959 14.083 1650 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.17 % Allowed : 7.52 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1536 helix: 0.81 (0.20), residues: 710 sheet: -1.94 (0.37), residues: 188 loop : -1.30 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 114 TYR 0.008 0.001 TYR A 340 PHE 0.014 0.001 PHE B 165 TRP 0.009 0.001 TRP B 557 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (11358) covalent geometry : angle 0.56493 / 0.28 (15522) SS BOND : bond 0.00143 / 0.09 ( 20) SS BOND : angle 0.52360 / 0.37 ( 40) hydrogen bonds : bond 0.02697 / 1.93 ( 524) hydrogen bonds : angle 4.55438 / 3.04 ( 1512) link_NAG-ASN : bond 0.00202 / 0.10 ( 4) link_NAG-ASN : angle 2.86959 / 1.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.441 Fit side-chains REVERT: A 72 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8940 (ppp) REVERT: A 202 MET cc_start: 0.9178 (mmt) cc_final: 0.8858 (mmt) REVERT: A 469 MET cc_start: 0.8746 (mmm) cc_final: 0.8481 (mmm) REVERT: A 778 MET cc_start: 0.8259 (mmm) cc_final: 0.7598 (tmm) REVERT: A 802 MET cc_start: 0.9315 (ttm) cc_final: 0.8937 (tmm) REVERT: B 72 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8943 (ppp) REVERT: B 202 MET cc_start: 0.9167 (mmt) cc_final: 0.8842 (mmt) REVERT: B 469 MET cc_start: 0.8719 (mmm) cc_final: 0.8472 (mmm) REVERT: B 778 MET cc_start: 0.8177 (mmm) cc_final: 0.7526 (tmm) REVERT: B 802 MET cc_start: 0.9311 (ttm) cc_final: 0.8932 (tmm) outliers start: 12 outliers final: 4 residues processed: 73 average time/residue: 0.0938 time to fit residues: 10.6706 Evaluate side-chains 67 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 153 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 56 optimal weight: 30.0000 chunk 141 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.059159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.040630 restraints weight = 75597.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041583 restraints weight = 42700.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.042024 restraints weight = 29233.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.042635 restraints weight = 24218.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.042860 restraints weight = 19856.077| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11382 Z= 0.239 Angle : 0.668 13.544 15574 Z= 0.334 Chirality : 0.043 0.143 1820 Planarity : 0.004 0.046 1992 Dihedral : 4.347 17.647 1650 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.78 % Allowed : 7.81 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1536 helix: 0.60 (0.19), residues: 708 sheet: -2.05 (0.35), residues: 192 loop : -1.33 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 465 TYR 0.010 0.001 TYR A 340 PHE 0.017 0.002 PHE B 363 TRP 0.018 0.002 TRP A 500 HIS 0.005 0.002 HIS B 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (11358) covalent geometry : angle 0.66258 / 0.33 (15522) SS BOND : bond 0.00211 / 0.13 ( 20) SS BOND : angle 0.59662 / 0.40 ( 40) hydrogen bonds : bond 0.03030 / 2.18 ( 524) hydrogen bonds : angle 4.87261 / 3.28 ( 1512) link_NAG-ASN : bond 0.00199 / 0.10 ( 4) link_NAG-ASN : angle 3.18266 / 2.02 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.436 Fit side-chains REVERT: A 72 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8968 (ppp) REVERT: A 202 MET cc_start: 0.9135 (mmt) cc_final: 0.8847 (mmt) REVERT: A 494 MET cc_start: 0.7661 (mmm) cc_final: 0.7275 (tpt) REVERT: A 778 MET cc_start: 0.8189 (mmm) cc_final: 0.7527 (tmm) REVERT: A 802 MET cc_start: 0.9291 (ttm) cc_final: 0.8931 (tmm) REVERT: A 818 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: B 72 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8935 (ppp) REVERT: B 202 MET cc_start: 0.9131 (mmt) cc_final: 0.8832 (mmt) REVERT: B 249 TYR cc_start: 0.8147 (t80) cc_final: 0.7720 (t80) REVERT: B 778 MET cc_start: 0.8128 (mmm) cc_final: 0.7479 (tmm) REVERT: B 802 MET cc_start: 0.9303 (ttm) cc_final: 0.8935 (tmm) REVERT: B 818 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8921 (m-80) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.0832 time to fit residues: 8.5532 Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 131 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.059940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041306 restraints weight = 74582.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.042299 restraints weight = 42463.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.042970 restraints weight = 29020.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043138 restraints weight = 22394.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.043621 restraints weight = 19921.829| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11382 Z= 0.148 Angle : 0.583 6.915 15574 Z= 0.291 Chirality : 0.042 0.133 1820 Planarity : 0.004 0.044 1992 Dihedral : 4.094 16.658 1650 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.78 % Allowed : 8.50 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.22), residues: 1536 helix: 0.91 (0.20), residues: 704 sheet: -2.05 (0.35), residues: 192 loop : -1.22 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 465 TYR 0.010 0.001 TYR A 340 PHE 0.014 0.001 PHE B 165 TRP 0.014 0.002 TRP A 500 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11358) covalent geometry : angle 0.57789 / 0.29 (15522) SS BOND : bond 0.00131 / 0.08 ( 20) SS BOND : angle 0.46472 / 0.32 ( 40) hydrogen bonds : bond 0.02612 / 1.87 ( 524) hydrogen bonds : angle 4.64388 / 3.10 ( 1512) link_NAG-ASN : bond 0.00222 / 0.11 ( 4) link_NAG-ASN : angle 2.95478 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.442 Fit side-chains REVERT: A 72 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8973 (ppp) REVERT: A 202 MET cc_start: 0.9223 (mmt) cc_final: 0.8917 (mmt) REVERT: A 469 MET cc_start: 0.8321 (tpp) cc_final: 0.7624 (tpp) REVERT: A 494 MET cc_start: 0.7713 (mmm) cc_final: 0.7053 (tpp) REVERT: A 720 MET cc_start: 0.9141 (ppp) cc_final: 0.8461 (pmm) REVERT: A 778 MET cc_start: 0.8124 (mmm) cc_final: 0.7536 (tmm) REVERT: A 802 MET cc_start: 0.9312 (ttm) cc_final: 0.8951 (tmm) REVERT: A 818 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: B 72 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8961 (ppp) REVERT: B 202 MET cc_start: 0.9224 (mmt) cc_final: 0.8910 (mmt) REVERT: B 249 TYR cc_start: 0.8090 (t80) cc_final: 0.7727 (t80) REVERT: B 469 MET cc_start: 0.8308 (tpp) cc_final: 0.7619 (tpp) REVERT: B 494 MET cc_start: 0.7638 (mmm) cc_final: 0.6981 (tpp) REVERT: B 720 MET cc_start: 0.9272 (tmm) cc_final: 0.8630 (pmm) REVERT: B 778 MET cc_start: 0.8102 (mmm) cc_final: 0.7503 (tmm) REVERT: B 802 MET cc_start: 0.9309 (ttm) cc_final: 0.8946 (tmm) REVERT: B 818 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8873 (m-80) outliers start: 8 outliers final: 4 residues processed: 64 average time/residue: 0.0827 time to fit residues: 8.7636 Evaluate side-chains 67 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 40.0000 chunk 88 optimal weight: 0.0370 chunk 123 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 95 optimal weight: 9.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.058689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040009 restraints weight = 75098.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041010 restraints weight = 43868.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.041674 restraints weight = 29764.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.042031 restraints weight = 23143.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.042352 restraints weight = 19989.921| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11382 Z= 0.254 Angle : 0.692 11.326 15574 Z= 0.346 Chirality : 0.044 0.140 1820 Planarity : 0.004 0.044 1992 Dihedral : 4.433 16.885 1650 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.78 % Allowed : 8.79 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1536 helix: 0.59 (0.19), residues: 708 sheet: -2.17 (0.35), residues: 194 loop : -1.31 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 465 TYR 0.010 0.001 TYR A 340 PHE 0.018 0.002 PHE A 363 TRP 0.012 0.002 TRP B 359 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.25 (11358) covalent geometry : angle 0.68614 / 0.34 (15522) SS BOND : bond 0.00217 / 0.13 ( 20) SS BOND : angle 0.58675 / 0.38 ( 40) hydrogen bonds : bond 0.03132 / 2.23 ( 524) hydrogen bonds : angle 5.01449 / 3.37 ( 1512) link_NAG-ASN : bond 0.00193 / 0.10 ( 4) link_NAG-ASN : angle 3.33642 / 2.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.448 Fit side-chains REVERT: A 72 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9102 (ppp) REVERT: A 202 MET cc_start: 0.9134 (mmt) cc_final: 0.8895 (mmt) REVERT: A 249 TYR cc_start: 0.8250 (t80) cc_final: 0.7695 (t80) REVERT: A 494 MET cc_start: 0.7711 (mmm) cc_final: 0.7142 (tpp) REVERT: A 720 MET cc_start: 0.8990 (ppp) cc_final: 0.8127 (mpp) REVERT: A 778 MET cc_start: 0.8129 (mmm) cc_final: 0.7324 (tpp) REVERT: A 802 MET cc_start: 0.9344 (ttm) cc_final: 0.9022 (tmm) REVERT: A 818 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: B 72 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.8945 (ppp) REVERT: B 202 MET cc_start: 0.9124 (mmt) cc_final: 0.8830 (mmt) REVERT: B 249 TYR cc_start: 0.8315 (t80) cc_final: 0.7818 (t80) REVERT: B 494 MET cc_start: 0.7722 (mmm) cc_final: 0.7162 (tpp) REVERT: B 778 MET cc_start: 0.8115 (mmm) cc_final: 0.7312 (tpp) REVERT: B 802 MET cc_start: 0.9355 (ttm) cc_final: 0.9031 (tmm) REVERT: B 818 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8948 (m-80) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.0804 time to fit residues: 8.2497 Evaluate side-chains 64 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 135 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.060082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.041414 restraints weight = 74299.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.042409 restraints weight = 43028.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.043119 restraints weight = 29158.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.043287 restraints weight = 22283.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.043772 restraints weight = 19716.498| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11382 Z= 0.132 Angle : 0.590 10.049 15574 Z= 0.292 Chirality : 0.041 0.131 1820 Planarity : 0.004 0.045 1992 Dihedral : 4.079 15.373 1650 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.78 % Allowed : 8.79 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.22), residues: 1536 helix: 1.03 (0.20), residues: 694 sheet: -2.34 (0.33), residues: 210 loop : -1.22 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 465 TYR 0.011 0.001 TYR A 340 PHE 0.013 0.001 PHE B 165 TRP 0.014 0.002 TRP A 500 HIS 0.002 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11358) covalent geometry : angle 0.58503 / 0.29 (15522) SS BOND : bond 0.00129 / 0.08 ( 20) SS BOND : angle 0.45584 / 0.30 ( 40) hydrogen bonds : bond 0.02625 / 1.88 ( 524) hydrogen bonds : angle 4.65091 / 3.11 ( 1512) link_NAG-ASN : bond 0.00240 / 0.12 ( 4) link_NAG-ASN : angle 2.98596 / 1.89 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3072 Ramachandran restraints generated. 1536 Oldfield, 0 Emsley, 1536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.410 Fit side-chains REVERT: A 72 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8989 (ppp) REVERT: A 202 MET cc_start: 0.9240 (mmt) cc_final: 0.8982 (mmt) REVERT: A 249 TYR cc_start: 0.8134 (t80) cc_final: 0.7727 (t80) REVERT: A 494 MET cc_start: 0.7733 (mmm) cc_final: 0.7170 (tpp) REVERT: A 720 MET cc_start: 0.8969 (ppp) cc_final: 0.8240 (mpp) REVERT: A 778 MET cc_start: 0.8119 (mmm) cc_final: 0.7559 (tmm) REVERT: A 802 MET cc_start: 0.9356 (ttm) cc_final: 0.9054 (tmm) REVERT: A 818 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8874 (m-80) REVERT: B 72 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.8987 (ppp) REVERT: B 202 MET cc_start: 0.9225 (mmt) cc_final: 0.8920 (mmt) REVERT: B 249 TYR cc_start: 0.8099 (t80) cc_final: 0.7741 (t80) REVERT: B 494 MET cc_start: 0.7721 (mmm) cc_final: 0.7158 (tpp) REVERT: B 720 MET cc_start: 0.9071 (tmm) cc_final: 0.8201 (mpp) REVERT: B 778 MET cc_start: 0.8102 (mmm) cc_final: 0.7307 (tpp) REVERT: B 802 MET cc_start: 0.9355 (ttm) cc_final: 0.9058 (tmm) REVERT: B 818 PHE cc_start: 0.9274 (OUTLIER) cc_final: 0.8875 (m-80) outliers start: 8 outliers final: 4 residues processed: 65 average time/residue: 0.0784 time to fit residues: 8.3976 Evaluate side-chains 65 residues out of total 1350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 818 PHE Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 818 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.058342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.039704 restraints weight = 76060.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.040625 restraints weight = 44136.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.041178 restraints weight = 29433.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.041687 restraints weight = 23336.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.041810 restraints weight = 19720.080| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11382 Z= 0.268 Angle : 0.712 13.800 15574 Z= 0.356 Chirality : 0.044 0.142 1820 Planarity : 0.004 0.046 1992 Dihedral : 4.471 16.830 1650 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.68 % Allowed : 9.38 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1536 helix: 0.56 (0.20), residues: 708 sheet: -2.31 (0.35), residues: 194 loop : -1.32 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 465 TYR 0.010 0.002 TYR A 340 PHE 0.019 0.002 PHE A 363 TRP 0.013 0.002 TRP B 359 HIS 0.006 0.002 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.27 (11358) covalent geometry : angle 0.70659 / 0.35 (15522) SS BOND : bond 0.00235 / 0.15 ( 20) SS BOND : angle 0.59987 / 0.40 ( 40) hydrogen bonds : bond 0.03143 / 2.23 ( 524) hydrogen bonds : angle 5.02459 / 3.40 ( 1512) link_NAG-ASN : bond 0.00169 / 0.09 ( 4) link_NAG-ASN : angle 3.39681 / 2.18 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1963.53 seconds wall clock time: 34 minutes 34.10 seconds (2074.10 seconds total)